<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"> <style>
	.KEYW {color: #933;}
	.COMM {color: #bbb; font-style: italic;}
	.NUMB {color: #393;}
	.STRN {color: #393;}
	.REGX {color: #339;}
	.line {border-right: 1px dotted #666; color: #666; font-style: normal;}
	</style></head><body><pre><span class='line'>  1</span> <span class="COMM">/**
<span class='line'>  2</span> * @lends Bio.Seq.primaryseq
<span class='line'>  3</span> */</span><span class="WHIT">
<span class='line'>  4</span> </span><span class="NAME">Bio.Seq.primaryseq</span><span class="WHIT"> </span><span class="PUNC">=</span><span class="WHIT"> </span><span class="NAME">Class.create</span><span class="PUNC">(</span><span class="NAME">Bio.Seq</span><span class="PUNC">,</span><span class="PUNC">{</span><span class="WHIT"> 
<span class='line'>  5</span>   </span><span class="COMM">/**
<span class='line'>  6</span>    * Bio.Seq.primaryseq
<span class='line'>  7</span>    * @author Lee Katz &lt;lskatz@gmail.com>
<span class='line'>  8</span>    * @class primary class for sequences
<span class='line'>  9</span>    * @constructs
<span class='line'> 10</span>    * @extends Bio.Seq
<span class='line'> 11</span>    */</span><span class="WHIT">
<span class='line'> 12</span> </span><span class="WHIT">  </span><span class="NAME">initialize</span><span class="PUNC">:</span><span class="WHIT"> </span><span class="KEYW">function</span><span class="PUNC">(</span><span class="NAME">$super</span><span class="PUNC">,</span><span class="NAME">args</span><span class="PUNC">)</span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 13</span> </span><span class="WHIT">    </span><span class="NAME">$super</span><span class="PUNC">(</span><span class="NAME">args</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 14</span> </span><span class="WHIT">    
<span class='line'> 15</span>     </span><span class="COMM">// mandatory arguments</span><span class="WHIT">
<span class='line'> 16</span> </span><span class="WHIT">    </span><span class="PUNC">[</span><span class="STRN">'seq'</span><span class="PUNC">,</span><span class="STRN">'id'</span><span class="PUNC">]</span><span class="PUNC">.</span><span class="NAME">each</span><span class="PUNC">(</span><span class="KEYW">function</span><span class="PUNC">(</span><span class="NAME">arg</span><span class="PUNC">)</span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 17</span> </span><span class="WHIT">      </span><span class="KEYW">if</span><span class="PUNC">(</span><span class="PUNC">!</span><span class="NAME">this.options</span><span class="PUNC">[</span><span class="NAME">arg</span><span class="PUNC">]</span><span class="PUNC">)</span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 18</span> </span><span class="WHIT">        </span><span class="NAME">this.throw</span><span class="PUNC">(</span><span class="STRN">"Argument "</span><span class="PUNC">+</span><span class="NAME">arg</span><span class="PUNC">+</span><span class="STRN">" is mandatory for this class"</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 19</span> </span><span class="WHIT">      </span><span class="PUNC">}</span><span class="WHIT">
<span class='line'> 20</span> </span><span class="WHIT">    </span><span class="PUNC">}</span><span class="PUNC">.</span><span class="NAME">bind</span><span class="PUNC">(</span><span class="KEYW">this</span><span class="PUNC">)</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 21</span> </span><span class="WHIT">    
<span class='line'> 22</span>     </span><span class="COMM">// remove any whitespace from the sequence</span><span class="WHIT">
<span class='line'> 23</span> </span><span class="WHIT">    </span><span class="NAME">this.options.seq</span><span class="PUNC">=</span><span class="NAME">this.options.seq.replace</span><span class="PUNC">(</span><span class="REGX">/\s+/</span><span class="PUNC">,</span><span class="STRN">""</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 24</span> </span><span class="WHIT">  </span><span class="PUNC">}</span><span class="PUNC">,</span><span class="WHIT">
<span class='line'> 25</span> </span><span class="WHIT">  </span><span class="COMM">/**
<span class='line'> 26</span>    * Return or update the sequence
<span class='line'> 27</span>    * @param seq If set, then updates the sequence
<span class='line'> 28</span>    */</span><span class="WHIT">
<span class='line'> 29</span> </span><span class="WHIT">  </span><span class="NAME">seq</span><span class="PUNC">:</span><span class="KEYW">function</span><span class="PUNC">(</span><span class="NAME">seq</span><span class="PUNC">)</span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 30</span> </span><span class="WHIT">    </span><span class="KEYW">if</span><span class="PUNC">(</span><span class="NAME">seq</span><span class="PUNC">)</span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 31</span> </span><span class="WHIT">      </span><span class="NAME">this.options.seq</span><span class="PUNC">=</span><span class="NAME">seq</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 32</span> </span><span class="WHIT">    </span><span class="PUNC">}</span><span class="WHIT">
<span class='line'> 33</span> </span><span class="WHIT">    </span><span class="KEYW">return</span><span class="WHIT"> </span><span class="NAME">this.options.seq</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 34</span> </span><span class="WHIT">  </span><span class="PUNC">}</span><span class="PUNC">,</span><span class="WHIT">
<span class='line'> 35</span> </span><span class="WHIT">  </span><span class="COMM">/**
<span class='line'> 36</span>    * Return or update the id
<span class='line'> 37</span>    * @param id If set, then updates the id
<span class='line'> 38</span>    */</span><span class="WHIT">
<span class='line'> 39</span> </span><span class="WHIT">  </span><span class="NAME">id</span><span class="PUNC">:</span><span class="KEYW">function</span><span class="PUNC">(</span><span class="NAME">id</span><span class="PUNC">)</span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 40</span> </span><span class="WHIT">    </span><span class="KEYW">if</span><span class="PUNC">(</span><span class="NAME">id</span><span class="PUNC">)</span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 41</span> </span><span class="WHIT">      </span><span class="NAME">this.options.id</span><span class="PUNC">=</span><span class="NAME">id</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 42</span> </span><span class="WHIT">    </span><span class="PUNC">}</span><span class="WHIT">
<span class='line'> 43</span> </span><span class="WHIT">    </span><span class="KEYW">return</span><span class="WHIT"> </span><span class="NAME">this.options.id</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 44</span> </span><span class="WHIT">  </span><span class="PUNC">}</span><span class="PUNC">,</span><span class="WHIT">
<span class='line'> 45</span> </span><span class="WHIT">  </span><span class="COMM">/**
<span class='line'> 46</span>    * Return or update the description
<span class='line'> 47</span>    * @param desc If set, then updates the description
<span class='line'> 48</span>    */</span><span class="WHIT">
<span class='line'> 49</span> </span><span class="WHIT">  </span><span class="NAME">desc</span><span class="PUNC">:</span><span class="KEYW">function</span><span class="PUNC">(</span><span class="NAME">desc</span><span class="PUNC">)</span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 50</span> </span><span class="WHIT">    </span><span class="KEYW">if</span><span class="PUNC">(</span><span class="NAME">desc</span><span class="PUNC">)</span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 51</span> </span><span class="WHIT">      </span><span class="NAME">this.options.desc</span><span class="PUNC">=</span><span class="NAME">desc</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 52</span> </span><span class="WHIT">    </span><span class="PUNC">}</span><span class="WHIT">
<span class='line'> 53</span> </span><span class="WHIT">    </span><span class="KEYW">return</span><span class="WHIT"> </span><span class="NAME">this.options.desc</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 54</span> </span><span class="WHIT">  </span><span class="PUNC">}</span><span class="PUNC">,</span><span class="WHIT">
<span class='line'> 55</span> </span><span class="WHIT">  </span><span class="NAME">alphabet</span><span class="PUNC">:</span><span class="KEYW">function</span><span class="PUNC">(</span><span class="NAME">alphabet</span><span class="PUNC">)</span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 56</span> </span><span class="WHIT">    </span><span class="KEYW">if</span><span class="PUNC">(</span><span class="NAME">alphabet</span><span class="PUNC">)</span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 57</span> </span><span class="WHIT">      </span><span class="NAME">this.options.alphabet</span><span class="PUNC">=</span><span class="NAME">alphabet</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 58</span> </span><span class="WHIT">    </span><span class="PUNC">}</span><span class="WHIT">
<span class='line'> 59</span> </span><span class="WHIT">    </span><span class="KEYW">return</span><span class="WHIT"> </span><span class="NAME">this.options.alphabet</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 60</span> </span><span class="WHIT">  </span><span class="PUNC">}</span><span class="PUNC">,</span><span class="WHIT">
<span class='line'> 61</span> </span><span class="WHIT">  </span><span class="NAME">toString</span><span class="PUNC">:</span><span class="KEYW">function</span><span class="PUNC">(</span><span class="PUNC">)</span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 62</span> </span><span class="WHIT">    </span><span class="KEYW">return</span><span class="WHIT"> </span><span class="NAME">this.fasta</span><span class="PUNC">(</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 63</span> </span><span class="WHIT">  </span><span class="PUNC">}</span><span class="PUNC">,</span><span class="WHIT">
<span class='line'> 64</span> </span><span class="WHIT">  </span><span class="COMM">/**
<span class='line'> 65</span>    * Return a fasta representation of the Seq
<span class='line'> 66</span>    * @returns String
<span class='line'> 67</span>    */</span><span class="WHIT">
<span class='line'> 68</span> </span><span class="WHIT">  </span><span class="NAME">fasta</span><span class="PUNC">:</span><span class="KEYW">function</span><span class="PUNC">(</span><span class="PUNC">)</span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 69</span> </span><span class="WHIT">    </span><span class="COMM">//var re = new RegExp("regex","g");</span><span class="WHIT">
<span class='line'> 70</span> </span><span class="WHIT">    </span><span class="KEYW">var</span><span class="WHIT"> </span><span class="NAME">fasta</span><span class="PUNC">=</span><span class="STRN">">"</span><span class="PUNC">+</span><span class="NAME">this.id</span><span class="PUNC">(</span><span class="PUNC">)</span><span class="PUNC">+</span><span class="STRN">" "</span><span class="PUNC">+</span><span class="NAME">this.desc</span><span class="PUNC">(</span><span class="PUNC">)</span><span class="PUNC">+</span><span class="NAME">this.nl</span><span class="WHIT">
<span class='line'> 71</span> </span><span class="WHIT">             </span><span class="COMM">// TODO make the width customizable</span><span class="WHIT">
<span class='line'> 72</span> </span><span class="WHIT">             </span><span class="PUNC">+</span><span class="NAME">this.seq</span><span class="PUNC">(</span><span class="PUNC">)</span><span class="PUNC">.</span><span class="NAME">replace</span><span class="PUNC">(</span><span class="REGX">/(.{60})/g</span><span class="PUNC">,</span><span class="STRN">"$1"</span><span class="PUNC">+</span><span class="NAME">this.nl</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 73</span> </span><span class="WHIT">    </span><span class="KEYW">return</span><span class="WHIT"> </span><span class="NAME">fasta</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 74</span> </span><span class="WHIT">  </span><span class="PUNC">}</span><span class="WHIT">
<span class='line'> 75</span> </span><span class="PUNC">}</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 76</span> </span></pre></body></html>